726 research outputs found
A stitch in time: Efficient computation of genomic DNA melting bubbles
Background: It is of biological interest to make genome-wide predictions of
the locations of DNA melting bubbles using statistical mechanics models.
Computationally, this poses the challenge that a generic search through all
combinations of bubble starts and ends is quadratic.
Results: An efficient algorithm is described, which shows that the time
complexity of the task is O(NlogN) rather than quadratic. The algorithm
exploits that bubble lengths may be limited, but without a prior assumption of
a maximal bubble length. No approximations, such as windowing, have been
introduced to reduce the time complexity. More than just finding the bubbles,
the algorithm produces a stitch profile, which is a probabilistic graphical
model of bubbles and helical regions. The algorithm applies a probability peak
finding method based on a hierarchical analysis of the energy barriers in the
Poland-Scheraga model.
Conclusions: Exact and fast computation of genomic stitch profiles is thus
feasible. Sequences of several megabases have been computed, only limited by
computer memory. Possible applications are the genome-wide comparisons of
bubbles with promotors, TSS, viral integration sites, and other melting-related
regions.Comment: 16 pages, 10 figure
Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens
A key question in evolutionary genetics is why certain mutations or certain types of mutation make disproportionate contributions to adaptive phenotypic evolution. In principle, the preferential fixation of particular mutations could stem directly from variation in the underlying rate of mutation to function-altering alleles. However, the influence of mutation bias on the genetic architecture of phenotypic evolution is difficult to evaluate because data on rates of mutation to function-altering alleles are seldom available. Here, we report the discovery that a single point mutation at a highly mutable site in the βA-globin gene has contributed to an evolutionary change in hemoglobin (Hb) function in high-altitude Andean house wrens (Troglodytes aedon). Results of experiments on native Hb variants and engineered, recombinant Hb mutants demonstrate that a nonsynonymous mutation at a CpG dinucleotide in the βA-globin gene is responsible for an evolved difference in Hb–O2 affinity between high- and low-altitude house wren populations. Moreover, patterns of genomic differentiation between high- and low-altitude populations suggest that altitudinal differentiation in allele frequencies at the causal amino acid polymorphism reflects a history of spatially varying selection. The experimental results highlight the influence of mutation rate on the genetic basis of phenotypic evolution by demonstrating that a large-effect allele at a highly mutable CpG site has promoted physiological differentiation in blood O2 transport capacity between house wren populations that are native to different elevations
Hydrology and water quality of a field and riparian buffer adjacent to a mangrove wetland in Jobos Bay watershed, Puerto Rico
Agriculture in coastal areas of Puerto Rico is often adjacent to or near mangrove wetlands. Riparian buffers, while they may also be wetlands, can be used to protect mangrove wetlands from agricultural inputs of sediment, nutrients, and pesticides. We used simulation models and field data to estimate the water, nitrogen, and phosphorus inputs from an agricultural field and riparian buffer to a mangrove wetland in Jobos Bay watershed, Puerto Rico. We used the Agricultural Policy/Environmental eXtender (APEX) and the Riparian Ecosystem Management Model (REMM) models sequentially to simulate the hydrology and water quality of the agricultural fields and an adjacent riparian buffer, respectively. Depth to the water table surface was measured monthly at numerous sites in both field and riparian areas and were used with recording well data from outside the field to estimate daily water table depths in the field and riparian buffer and to calibrate field-scale hydrologic processes. Calibration and validation of the models were successful for the riparian buffer and in three of four field quadrants. In these areas the average simulated depth to water table for the field and the riparian buffer were within ±7% of field estimated water table depths. Over the 3-year study period, the riparian buffer represented by REMM reduced agricultural loadings to the mangrove wetland by 24% for sediment yield, and about 30% for total nitrogen and phosphorus. Simulations indicated that tropical storms and hurricanes played an important role in water and nutrient transport on this site contributing at least 63% of total sediment and nutrient loads
Increasing the Creativity of ENGINO Toy Sets and Generating Automatic Building Instructions
During the First Study Group with Industry which was held in Limassol, Cyprus, the ENGINO⃝R TOY SYSTEM introduced two challenging problems. The first is to get bounds on the number of possible models/toys which can be constructed using a given package of building blocks. And the second is to generate automatically the assembly instructions for a given toy. In this report we summarize our insights and provide preliminary results for the two challenges
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LDRD summary report. Part 1: initiation studies of thin film explosvies used for scabbling concrete. Part 2: investigation of spray techniques for use in explosive scabbling of concrete
We describe a new method for the scabbling of concrete surfaces using a thin layer of explosive material sprayed onto the surfaces. We also developed a new explosive mixture that could be applied with commercial spray painting equipment. The first part of our record describes experiments that studied methods for the initiation of the sprayed explosive. We successfully initiated layers 0.36 mm thick using a commercial EBW detonator, a flying plate detonator, and by pellet impact. The second part of our report describes a survey of spray methods and tests with two commercial spray systems that we believe could be used for developing a robotic spray system
Salerno's model of DNA reanalysed: could solitons have biological significance?
We investigate the sequence-dependent behaviour of localised excitations in a
toy, nonlinear model of DNA base-pair opening originally proposed by Salerno.
Specifically we ask whether ``breather'' solitons could play a role in the
facilitated location of promoters by RNA polymerase. In an effective potential
formalism, we find excellent correlation between potential minima and {\em
Escherichia coli} promoter recognition sites in the T7 bacteriophage genome.
Evidence for a similar relationship between phage promoters and downstream
coding regions is found and alternative reasons for links between AT richness
and transcriptionally-significant sites are discussed. Consideration of the
soliton energy of translocation provides a novel dynamical picture of sliding:
steep potential gradients correspond to deterministic motion, while ``flat''
regions, corresponding to homogeneous AT or GC content, are governed by random,
thermal motion. Finally we demonstrate an interesting equivalence between
planar, breather solitons and the helical motion of a sliding protein
``particle'' about a bent DNA axis.Comment: Latex file 20 pages, 5 figures. Manuscript of paper to appear in J.
Biol. Phys., accepted 02/09/0
DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism
Inverted repeat (IR) sequences in DNA can form non-canonical cruciform
structures to relieve torsional stress. We use Monte Carlo simulations of a
recently developed coarse-grained model of DNA to demonstrate that the
nucleation of a cruciform can proceed through a cooperative mechanism. Firstly,
a twist-induced denaturation bubble must diffuse so that its midpoint is near
the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must
be large enough to allow one of the arms to form a small number of hairpin
bonds. Once the first arm is partially formed, the second arm can rapidly grow
to a similar size. Because bubbles can twist back on themselves, they need
considerably fewer bases to resolve torsional stress than the final cruciform
state does. The initially stabilised cruciform therefore continues to grow,
which typically proceeds synchronously, reminiscent of the S-type mechanism of
cruciform formation. By using umbrella sampling techniques we calculate, for
different temperatures and superhelical densities, the free energy as a
function of the number of bonds in each cruciform along the correlated but
non-synchronous nucleation pathways we observed in direct simulations.Comment: 12 pages main paper + 11 pages supplementary dat
Complex life forms may arise from electrical processes
There is still not an appealing and testable model to explain how single-celled organisms, usually following fusion of male and female gametes, proceed to grow and evolve into multi-cellular, complexly differentiated systems, a particular species following virtually an invariant and unique growth pattern. An intrinsic electrical oscillator, resembling the cardiac pacemaker, may explain the process. Highly auto-correlated, it could live independently of ordinary thermodynamic processes which mandate increasing disorder, and could coordinate growth and differentiation of organ anlage
Dynamics of liquid 4He in Vycor
We have measured the dynamic structure factor of liquid 4He in Vycor using
neutron inelastic scattering. Well-defined phonon-roton (p-r) excitations are
observed in the superfluid phase for all wave vectors 0.3 < Q < 2.15. The p-r
energies and lifetimes at low temperature (T = 0.5 K) and their temperature
dependence are the same as in bulk liquid 4He. However, the weight of the
single p-r component does not scale with the superfluid fraction (SF) as it
does in the bulk. In particular, we observe a p-r excitation between T_c =
1.952 K, where SF = 0, and T_(lambda)=2.172 K of the bulk. This suggests, if
the p-r excitation intensity scales with the Bose condensate, that there is a
separation of the Bose-Einstein condensation temperature and the superfluid
transition temperature T_c of 4He in Vycor. We also observe a two-dimensional
layer mode near the roton wave vector. Its dispersion is consistent with
specific heat and SF measurements and with layer modes observed on graphite
surfaces.Comment: 3 pages, 4 figure
Ornithological expeditions to Sarawak, Malaysian Borneo, 2007-2017
Louisiana State University, the University of Kansas, and the Universiti Malaysia Sarawak undertook collaborative research on the evolution and ecology of Bornean birds starting in 2005. This collaboration included a series of expeditions from 2007–2017 to collect and study birds at \u3e30 sites in Sarawak, Malaysian Borneo. Here we provide information on the study-sites and summarize the main discoveries resulting from the collaboration
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